Mutagenetix > Incidental Mutation

Incidental Mutation 'R0257:Vps53'

34794

Institutional Source

Beutler Lab

Gene Symbol

Vps53

Ensembl Gene

ENSMUSG00000017288

Gene Name

VPS53 GARP complex subunit

Synonyms

2310040I21Rik, 3100002B05Rik, 2010002A08Rik

MMRRC Submission

038488-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0257 (G1)

Quality Score

127

Status

Validated

Chromosome

Chromosomal Location

76046226-76179647 bp(-) (GRCm38)

Type of Mutation

intron

DNA Base Change (assembly)

A to T at 76177385 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000127364 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000129256] [ENSMUST00000129853] [ENSMUST00000163878] [ENSMUST00000166752] [ENSMUST00000167114] [ENSMUST00000169734] [ENSMUST00000170730]

AlphaFold

Q8CCB4

Predicted Effect

probably benign
Transcript: ENSMUST00000056601

SMART Domains

Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	5.9e-11	PFAM
Pfam:Vps53_N	39	453	1.9e-176	PFAM
low complexity region	520	533	N/A	INTRINSIC
low complexity region	820	832	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000094015

SMART Domains

Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	96	6.2e-21	PFAM
Pfam:Vps53_N	93	424	1.4e-133	PFAM
low complexity region	491	504	N/A	INTRINSIC
low complexity region	791	803	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108419

SMART Domains

Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	224	4e-11	PFAM
Pfam:Vps53_N	39	233	5.2e-87	PFAM
Pfam:Vps53_N	226	276	1.6e-14	PFAM
low complexity region	343	356	N/A	INTRINSIC
low complexity region	643	655	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127340

Predicted Effect

probably benign
Transcript: ENSMUST00000129256

Predicted Effect

probably benign
Transcript: ENSMUST00000129853

SMART Domains

Protein: ENSMUSP00000114936
Gene: ENSMUSG00000069808

Domain	Start	End	E-Value	Type
TLC	1	166	6.2e-8	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140886

Predicted Effect

probably benign
Transcript: ENSMUST00000163878

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166084

Predicted Effect

probably benign
Transcript: ENSMUST00000166752

SMART Domains

Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	8.2e-12	PFAM
Pfam:Vps53_N	39	230	6e-87	PFAM
Pfam:Vps53_N	226	405	1.4e-60	PFAM
low complexity region	472	485	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170143

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169532

Predicted Effect

probably benign
Transcript: ENSMUST00000167114

SMART Domains

Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	101	1.2e-21	PFAM
Pfam:Vps53_N	104	176	3.1e-15	PFAM
low complexity region	243	256	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000169734

SMART Domains

Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
Pfam:DUF2450	5	225	5.1e-12	PFAM
Pfam:Vps53_N	39	329	1e-137	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000170730

SMART Domains

Protein: ENSMUSP00000127364
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	54	123	3e-34	PFAM

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 98.5%
3x: 97.5%
10x: 95.7%
20x: 92.2%

Validation Efficiency

99% (67/68)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E12.5 with trophoblast cell hyperplasia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700061G19Rik	T	A	17: 56,885,169	Y577*	probably null	Het
Aatf	T	A	11: 84,510,281	E171D	probably benign	Het
Adgre5	T	A	8: 83,731,995	H134L	possibly damaging	Het
Ahsg	A	T	16: 22,899,040	M256L	probably benign	Het
Alk	A	T	17: 72,603,495	L72Q	probably damaging	Het
Ano2	C	A	6: 125,880,713	A505E	probably benign	Het
Bcas3	A	G	11: 85,822,039	K908E	probably benign	Het
C3ar1	A	G	6: 122,850,787	V157A	probably benign	Het
Car2	C	G	3: 14,899,977	H224D	probably benign	Het
Cfh	T	C	1: 140,144,035	D287G	probably benign	Het
Disp3	G	T	4: 148,250,754	N944K	possibly damaging	Het
Dlg1	A	G	16: 31,842,853		probably benign	Het
Dmbt1	A	G	7: 131,106,393	E1281G	probably damaging	Het
Dmxl1	T	A	18: 49,955,803		probably benign	Het
Dtx3	T	C	10: 127,192,892	D159G	probably benign	Het
Ets2	T	A	16: 95,712,201	C140*	probably null	Het
Fbf1	T	C	11: 116,155,091	I226V	probably benign	Het
Fgd6	T	A	10: 94,043,915	H210Q	probably benign	Het
Fktn	A	G	4: 53,734,898	T179A	probably benign	Het
Galnt10	T	C	11: 57,781,078	M398T	probably damaging	Het
Grk5	G	T	19: 61,076,630		probably benign	Het
Gse1	A	G	8: 120,572,334		probably benign	Het
Hmcn2	T	C	2: 31,369,164		probably benign	Het
Iqgap2	A	G	13: 95,724,544		probably null	Het
Lama4	T	C	10: 39,094,884		probably benign	Het
Luzp2	A	G	7: 55,249,446	T271A	probably benign	Het
Mdn1	T	A	4: 32,693,534	V1053D	probably damaging	Het
Mrm1	A	C	11: 84,814,823		probably benign	Het
Msh5	G	C	17: 35,032,864	R407G	probably damaging	Het
Myo1c	A	T	11: 75,665,516		probably null	Het
Nek5	T	C	8: 22,123,672		probably benign	Het
Nrxn2	A	G	19: 6,490,698	I894V	possibly damaging	Het
Olfr372	C	T	8: 72,058,400	T240M	probably damaging	Het
Pde4a	C	T	9: 21,192,421	P175L	probably damaging	Het
Pip5k1c	C	A	10: 81,315,096	A628E	possibly damaging	Het
Piwil2	C	T	14: 70,422,631	S139N	probably benign	Het
Prob1	T	C	18: 35,653,039	K721E	possibly damaging	Het
Rps6ka2	C	A	17: 7,227,983	S57Y	probably damaging	Het
Rxfp1	C	T	3: 79,682,535	V100M	possibly damaging	Het
Serpinb9e	A	T	13: 33,257,681	M199L	probably benign	Het
Slc17a3	C	T	13: 23,855,858	S293F	probably damaging	Het
Slc4a8	G	A	15: 100,784,880		probably benign	Het
Sned1	A	T	1: 93,265,097	S369C	possibly damaging	Het
St18	T	A	1: 6,819,962	F539L	probably benign	Het
Stam2	C	T	2: 52,694,782	G500D	possibly damaging	Het
Stx16	G	A	2: 174,096,961	V307M	probably benign	Het
Svep1	G	A	4: 58,179,610	S211L	possibly damaging	Het
Tcf12	C	T	9: 71,858,622	S512N	probably benign	Het
Tiam2	T	C	17: 3,450,813	V909A	possibly damaging	Het
Tmem64	C	T	4: 15,266,343	A131V	probably damaging	Het
Tnrc6b	C	A	15: 80,894,355	N1176K	possibly damaging	Het
Trrap	C	T	5: 144,804,235	S1264L	probably benign	Het
Ttn	T	A	2: 76,810,431	T13658S	possibly damaging	Het
Vmn2r104	G	A	17: 20,029,627	T794I	probably damaging	Het
Vmn2r52	T	A	7: 10,171,055	R286*	probably null	Het
Wdr18	A	G	10: 79,961,119		probably benign	Het
Wdr31	A	G	4: 62,460,518		probably null	Het
Zfp458	T	A	13: 67,259,642	K47*	probably null	Het
Zfp983	A	G	17: 21,661,440	T95A	probably benign	Het

Other mutations in Vps53

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00475:Vps53	APN	11	76077035	splice site	probably null
IGL01596:Vps53	APN	11	76063037	missense	probably damaging	1.00
IGL01655:Vps53	APN	11	76063034	missense	probably damaging	0.97
IGL02275:Vps53	APN	11	76047123	missense	probably benign	0.03
IGL02321:Vps53	APN	11	76048538	missense	possibly damaging	0.60
IGL02581:Vps53	APN	11	76102057	missense	probably damaging	0.99
IGL02821:Vps53	APN	11	76136317	splice site	probably benign
IGL02958:Vps53	APN	11	76117711	missense	probably damaging	1.00
IGL03001:Vps53	APN	11	76138324	missense	probably damaging	1.00
PIT4519001:Vps53	UTSW	11	76117173	missense	probably damaging	1.00
R0391:Vps53	UTSW	11	76121579	missense	probably benign	0.31
R0421:Vps53	UTSW	11	76082670	missense	probably damaging	1.00
R0882:Vps53	UTSW	11	76082659	missense	probably damaging	1.00
R2509:Vps53	UTSW	11	76066835	missense	possibly damaging	0.49
R3622:Vps53	UTSW	11	76117783	missense	probably benign	0.00
R5137:Vps53	UTSW	11	76166248	missense	probably damaging	1.00
R5338:Vps53	UTSW	11	76081208	missense	probably damaging	1.00
R5756:Vps53	UTSW	11	76092330	splice site	probably benign
R5786:Vps53	UTSW	11	76063007	missense	probably benign	0.08
R5961:Vps53	UTSW	11	76048490	missense	probably damaging	1.00
R6059:Vps53	UTSW	11	76066867	missense	possibly damaging	0.57
R6273:Vps53	UTSW	11	76102018	missense	probably benign	0.16
R6490:Vps53	UTSW	11	76077055	missense	probably benign	0.03
R6657:Vps53	UTSW	11	76134427	missense	probably damaging	1.00
R6671:Vps53	UTSW	11	76134506	missense	probably damaging	1.00
R6772:Vps53	UTSW	11	76179498	start codon destroyed	probably null
R7378:Vps53	UTSW	11	76077074	missense	possibly damaging	0.88
R7735:Vps53	UTSW	11	76047136	missense	probably damaging	1.00
R8066:Vps53	UTSW	11	76136307	missense	probably damaging	1.00
Z1177:Vps53	UTSW	11	76136198	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- CCTGTCATTGTGAGCTGGTATGAGGAA -3'
(R):5'- CTTGTTGGGAAGAGAAGACTCTTAGGGA -3'

Sequencing Primer
(F):5'- AGTGGGTTATTCACTTCCTAACTG -3'
(R):5'- agccatttcaccagccc -3'

Posted On

2013-05-09